There seems to be some remaining adapter in some of the library reads.

Overall I've ended up with about 235,011,160 read pairs from the whole lane after deduplicating and trimming.

Other info: library preparation was PCR-free using physically sheared DNA; Inserts were sized by gel purification; Libraries were dual indexed.

My questions are:

1. Is this quality/quantity typical from a commercial provider for this platform?
2. Is the sequence bias observed at the 5' end of the reads observed in these libraries typical for a PCR-free library generated from physically sheared fragments?